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Series GSE68087 Query DataSets for GSE68087
Status Public on Jan 29, 2016
Title Active DNA demethylation at enhancers during the vertebrate phylotypic period
Organisms Danio rerio; Xenopus tropicalis; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the epigenome through this transition and their evolutionary conservation remain elusive. Here we report widespread DNA demethylation of enhancers during the phylotypic period in zebrafish, Xenopus and mouse. These enhancers are linked to developmental genes that display coordinated transcriptional and epigenomic changes in the diverse vertebrates during embryogenesis. Binding of Tet proteins to (hydroxy)methylated DNA, and enrichment of hydroxymethylcytosine on these regions, implicated active DNA demethylation in this process. Furthermore, loss of function of Tet1/2/3 in zebrafish caused reduced chromatin accessibility and increased methylation levels specifically on these enhancers, indicative of DNA methylation being an upstream regulator of phylotypic enhancer function. Overall, our study reveals a novel regulatory module associated with the most conserved phase of vertebrate embryogenesis and uncovers an ancient developmental role for the Tet dioxygenases.
Overall design MethylC-Seq in zebrafish embryos, MethylC-seq in Xenopus tropicalis embryos, MethylC-seq in mouse embryos, MethylC-seq in zebrafish tissues, MethylC-seq in Xenopus tropicalis tissues, TAB-seq in zebrafish embryos, TAB-seq in Xenopus tropicalis embryos, TAB-seq in mouse embryos, RNA-seq in zebrafish embryos, RNA-seq in mouse embryos
Contributor(s) Bogdanovic O, Lister R
Citation(s) 26928226
Submission date Apr 21, 2015
Last update date May 15, 2019
Contact name Ozren Bogdanovic
Organization name Garvan Institute of Medical Research
Department Genomics and Epigenetics
Street address 384 Victoria Street
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
Platforms (4)
GPL14875 Illumina HiSeq 2000 (Danio rerio)
GPL18171 Illumina HiSeq 1500 (Danio rerio)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (30)
GSM1662779 MethylC-Seq_dr_epiboly
GSM1662780 MethylC-Seq_dr_24hpf
GSM1662781 MethylC-Seq_dr_48hpf
BioProject PRJNA281741
SRA SRP057505

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Supplementary file Size Download File type/resource
GSE68087_RAW.tar 29.2 Gb (http)(custom) TAR (of BED, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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